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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatgagcaacaataatatttcaaagcagtatgaccctattgtcttgcctatcaaaaagatttcgccctattgtctttggttgtttatacttaaa...

Basic information

species Vitis vinifera
transcript Vv11s0016g03530.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g41040.1 (Oryza sativa), 5'ss of exon 3
GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtc-agtgatgagcaacaataatatt-tcaaagcagta-tgaccctattgtcttgcctatcaaaaagatttcgccctattgtctttggttgtttatacttaaa--
 || ||||| || || |||   ||||| || |||||  || | |||||   |||| ||||||||||  |||||||| |||||||||||||||| || ||||||  |  ||   ||    | || || ||| ||  ||| |      ||||  |||   | || || |   |||   | |  |   ||  |||| |||  |  |  
TGTGAACATTAAGGATCATACCCTTGTGCCAGAGCACGAGCTCCTGACGCCTGAGCAGAAGAAGACGCTGCTGGAGCGGTATACCGTGAAAGAGACTCAGgtctggaaatagacattttttattttctcataggtgtagtatttgaattgatttg---agcataatgtcatcgatgtttcattcatg--tgttgatatctgcaca

upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g59140.1 (Oryza sativa), 5'ss of exon 3
GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgt-cagtgatgagcaacaataatatttcaaagcagtatgaccctattgtcttgcctatcaaaaagat-ttcgccctattgtctttggttgtttatacttaaa-
  | || ||||| ||||||||||| |||||||| ||||| ||||| | || |||||| |||||||| ||  ||||| |||| ||  | || ||||| |||||   |  |   |      |   | || |    | ||||    |  | ||      | |||  |  |    ||  |  |  | | |    ||       ||| 
TATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTCTAAAGGAAACTCAGgtattgccacttgtggacttgcaacttta---taatatgcttttggtatcagaggaaccaaccatttacgtgctttcctaacatagcaatttcggggacaaaa

upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G476009_T01 (Zea mays), 5'ss of exon 3
GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatgagcaacaataatatttcaaagcagtatgaccctattgtcttgcctatcaaaaagatttcgccctattgt-----ctttggttgtttatacttaaa
  | |||||||| |||||||| ||||||||||||||||||||||| || |  ||||||||||||||  | |||||| |||| ||| |||| ||||| ||||| | ||  |  ||   | | |  | || | |  ||| ||    |  |||   | |       |  |  | || |   |      ||    | | ||||      
TATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCTTGAAGGAAACTCAGgt-attggcgctcattcacact--tacagatctttattactac-tactctcagccagtggggggcatcagaccaaacataaaagtttcaactttctatagcctg-

upper sequence: Vv11s0016g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G22320.1 (Arabidopsis thaliana), 5'ss of exon 4
GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatgagcaacaataatatttcaaagc--agt-atgaccctattgtcttgcctatcaaaaagatttcgccctattgtctttggttgtttatacttaaa
 || ||||| ||||||||||||||||||||||||||||| || || |||| ||| |||||||| ||||| |||||||| || || ||||| || |||||||| |||  |    |  ||   | ||| ||  |   || ||||   | ||||  ||  ||| |||    |    |  | | |   ||| | |            
AGTGAACATTAAAGAACATGTTCTTGTTCCTGAGCATCAAGTTCTTACCACTGAAGAGAAGAAAACTTTACTGGAGAGATACACAGTGAAGGAGACACAGgttagtagtatatagaaactttgtttgaattcttggtgatgaaatttttgttgtgt-tattaaatgtttggaactttgtgggtgttgttag------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351022956|gb|FQ428865.1|FQ428865
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAG                         CTACCTCGAATTCAAGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|352791437|gb|FQ481016.1|FQ481016
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAAGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|30252036|gb|CB968675.1|CB968675
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|30329733|gb|CD012995.1|CD012995
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351013267|gb|FQ424972.1|FQ424972
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351013686|gb|FQ433838.1|FQ433838
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|33404617|gb|CF210244.1|CF210244
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|27585125|gb|CB007820.1|CB007820
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAAT
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAAT
EST: gi|161713942|gb|FC062890.1|FC062890
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAG                         CTACCTTGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351014433|gb|FQ437435.1|FQ437435
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAGGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351033523|gb|FQ446989.1|FQ446989
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351041122|gb|FQ444099.1|FQ444099
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|349822801|gb|FQ398188.1|FQ398188
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGAAATTTCGGGCTGAAA
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351022411|gb|FQ445186.1|FQ445186
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAC
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|349818759|gb|FQ409293.1|FQ409293
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAGACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATCTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|351043644|gb|FQ451575.1|FQ451575
EST:     GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG
EST: gi|349820033|gb|FQ404755.1|FQ404755
EST:     GTGAGGAGAATAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAG                         CTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCCGGCTGAAG
genomic: GTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatg ... cttcttttagCTACCTCGAATTCAGGTGAGCGACCCGATTGCAAGATATTTCGGGCTGAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCGTGAAAGAAACACAGgtcagtgatgagcaacaataatatttcaaagcagtatgaccctattgtcttgcctatcaaaaagatttcgccctattgtctttggttgtttatacttaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga